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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggctttgcagttccagataaagaagcctttgactctttgtcgtgtttaagtgtttctgtttggaaaaacttcttactgaatgtttaccgaatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT

Basic information

species Zea mays
transcript GRMZM2G060896_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060896_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g15550.2 (Oryza sativa), 3'ss of exon 9
aggctttgcagttccagataaagaagcctttgactctttgtcgtgtttaagtgtttctgtttggaaaaacttcttactgaatgtttaccgaat----ctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT
  || |       | |||| | |     ||  | |  |  |         |      ||||||||      | |||    |  ||||     |     | ||||||| |||||||| ||| | |||||||||||||||||||||   || ||||| |||||||||  ||||||||||||||| || ||||||||||   |||| 
--gcataaatcgcctagatgatgt--ttttcaagtggtaattactggcttgccgcaatgtttggagttcacttttaacatacatttattcctttgcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTTCCTGACTCCTGCAAATCCAATTGAAAAACTAGAAGGAGCTATGGAAGCA

upper sequence: GRMZM2G060896_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g15550.3 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------------------------------aggctttgcagttccagataaagaagccttt-gactctttgtcgtgtttaagtgtttctgtttggaaaaacttcttactgaatgtttaccgaatc----tcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT
                                                                                 | |||    |  ||      | || |  |||  | |  |  |         |      ||||||||      | |||    |  ||||     |     | ||||||| |||||||| ||| | |||||||||||||||||||||   || ||||| |||||||||  ||||||||||||||| || ||||||||||   |||| 
gttagacagttggttgcgattctttttattgtgtattaagctcattgctccactgttttaatatggtgaaagtgaagcattaagctgcataaatcgcctagatgatgtttttcaagtggtaattactggcttgccgcaatgtttggagttcacttttaacatacatttattcctttgcatttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTTCCTGACTCCTGCAAATCCAATTGAAAAACTAGAAGGAGCTATGGAAGCA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|5819350|gb|AI987556.1|AI987556
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|5714138|gb|AI944123.1|AI944123
EST:     GGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGT-AACTT
genomic: GGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|45567480|gb|CK985592.1|CK985592
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|5847113|gb|AW000192.1|AW000192
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|40303182|gb|CK347569.1|CK347569
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|37394872|gb|CF634714.1|CF634714
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|6056688|gb|AW091093.1|AW091093
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|5597203|gb|AI891196.1|AI891196
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGACCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|37390214|gb|CF632335.1|CF632335
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|6095484|gb|AW120151.1|AW120151
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|71305268|gb|DR788768.1|DR788768
EST:     TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTATTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|32850727|gb|CD990408.1|CD990408
EST:     ACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: ACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|5525664|gb|AI861557.1|AI861557
EST:     TTCAAGGGTTCTGTACGCTATGCATGGGCAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAAAAGGTCCATTGGTGAACTT
genomic: TTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
EST: gi|37389864|gb|CF632156.1|CF632156
EST:     AGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT
genomic: AGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 72

GGTTACATACACATTTGATTCAGGATATGCTTTCAATTTGCCGTGAAACTTTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GGTTACATACACATTTGATTCAGGATATGCTTTCAATTTGCCGTGAAACTTTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GGTTACATACACATTTGATTCAGGATATGCTTTCAATTTGCCGTGAAACTTTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 51

GGTTACATACACATTTGATTCAGGATATGCTTTCAATTTGCCGTGAAACTTTCAAGGGTTCTGTACGCTATGCATGGACAAGTGTCCCAACATACCCGAGgttggttctt ... aatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagtgtttctgtttggaaaaacttcttactgaatgtttaccgaatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT
                         ttcttac  putative branch site (score: 51)
                   aaaaactt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggctttgcagttccagataaagaagcctttgactctttgtcgtgtttaagtgtttctgtttggaaaaacttcttactgaatgtttaccgaatctcgcagTGGGGTGATTGGATTTTTACTATGTGCCAAAGAAGGTCCATTGGTGAACTTTCTGACTCCTATAAATCCAATTGAAAAGCTGGAAGGAGCTACAAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT